CSA_alignedMetaSpectraCataloger

This function generates integrated and most abundant aligned spectra from the aligned spectra

A fragmentation spectra detection pipeline for high-throughput LC/HRMS data processing using peaklists generated by the 'IDSL.IPA' workflow <doi:10.1021/acs.jproteome.2c00120>. The 'IDSL.CSA' package can deconvolute fragmentation spectra from Composite Spectra Analysis (CSA), Data Dependent Acquisition (DDA) analysis, and various Data-Independent Acquisition (DIA) methods such as MS^E, All-Ion Fragmentation (AIF) and SWATH-MS analysis. The 'IDSL.CSA' package was introduced in <doi:10.1021/acs.analchem.3c00376>.

Dinesh Barupal

IDSL.CSA

Composite Spectra Analysis (CSA) for High-Resolution Mass
Spectrometry Analyses

Sadjad Fakouri-Baygi

CSA_alignedMetaSpectraCataloger function

<dl> <dt>address_input_msp</dt>
<dd>address of the .msp files generated via IDSL.IPA DIA grouping</dd> <dt>peakXcol</dt>
<dd>aligned indexed peak table</dd> <dt>peak_height</dt>
<dd>aligned peak height table</dd> <dt>CSA_aligned_property_table</dt>
<dd>a matrix of three columns of "IPA detection frequency", "median_height", and "median_R13C" for the aligned peak table</dd> <dt>groupedID</dt>
<dd>A 2-column dataframe of `Co-detectedIDs` and `TanimotoCoefficients` from the `CSA_alignedPeaksTanimotoCoefficientCalculator` module</dd> <dt>minTanimotoCoefficient</dt>
<dd>minimum Tanimoto coefficient</dd> <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd></dl>

Arguments

CSA Aligned Meta-Spectra Cataloger — CSA_alignedMetaSpectraCataloger

<dl>

 <dt>address_input_msp</dt>
<dd>address of the .msp files generated via IDSL.IPA DIA grouping</dd>

 <dt>peakXcol</dt>
<dd>aligned indexed peak table</dd>

 <dt>peak_height</dt>
<dd>aligned peak height table</dd>

 <dt>CSA_aligned_property_table</dt>
<dd>a matrix of three columns of "IPA detection frequency", "median_height", and "median_R13C" for the aligned peak table</dd>

 <dt>groupedID</dt>
<dd>A 2-column dataframe of `Co-detectedIDs` and `TanimotoCoefficients` from the `CSA_alignedPeaksTanimotoCoefficientCalculator` module</dd>

 <dt>minTanimotoCoefficient</dt>
<dd>minimum Tanimoto coefficient</dd>

 <dt>number_processing_threads</dt>
<dd>Number of processing threads for multi-threaded processing</dd>

</dl>

CSA_alignedMetaSpectraCataloger: CSA Aligned Meta-Spectra Cataloger

Description

Usage

Value

Arguments